THE HOLY is the 35th track on the DELTARUNE Chapter 1 OST.
The only times it plays is during Chapter 1's Dark Fountain scene,
and Chapter 2's normal route Dark Fountain scene.

As far as I can tell, there doesn't seem to be any clear meaning behind this song and its motifs.
This page doesn't aim to find the meaning of THE HOLY, and to instead assist in finding THE HOLY's meaning.

THE HOLY'S CONTENTS

THE HOLY is played at 140 BPM, in the key of D Minor.
The song consists of 3 different sections, with each section having its own appearance in other songs.

Section A is the following:
A 2-note repeating pattern, with both notes being of equal length.

Section A appears in the following songs:

CH1 & 2: 40 / 46. Before the Story

(Flute part that fades in. Debatable, not all intervals are the same and there's frequent modulation, however it can be argued as evoking THE HOLY.)

CH3+4: 33. SWORD

(Two-note repeating pattern of same-length notes in accompaniment. Shares the exact same interval (major 2nd) as THE HOLY.)

CH3+4: 48. ATRIUM

(Debatable? It's hard to make out the 2-note pattern but it could be argued there is one there in that crescendo)

CH3+4: 55. Ever Higher

(Sounds extremely similar, biggest difference being the instrumentation, likely to fit in with Ever Higher's style. Plays underneath the main melody.)

Section B is the following:
Section A, with an added vocal melody.

Section B appears in the following songs:

CH3+4: 1. Flashback (Excerpt)

(Played on the detuned synth pad that is audible under the melody. Exact same contour and possibly intervals, only modulated down to this song's key)

Section C is the following:
Also Section A, with a different melody.

Note: this melody, although similar, is not Penumbra Phantasm.

Section C appears in the following songs:

CH3+4: 32. Dump

(Played on a glockenspiel as a counter-melody. Practically identical to the melody presented in THE HOLY.)

It is a common misconception that THE HOLY contains Penumbra Phantasm.
Penumbra Phantasm was originally a song composed for Homestuck, and although it was never finished, its motif was still used in songs in Homestuck.
As Toby Fox has stated before, no music composed primarily for Homestuck will be used in DELTARUNE.
It is possible Penumbra Phantasm was meant to be used in DELTARUNE, but Toby Fox chose against it as it may feel a bit out of place with its Homestuck context.
It is very possible that THE HOLY's melody was meant to be similar to Penumbra Phantasm.

The glockenspiel part is THE HOLY's melody.
The xylophone part is Penumbra Phantasm's melody.

For those unable to read sheet music, THE HOLY's melody goes down then up, whereas Penumbra Phantasm goes up then down.
They only share three exact notes, and one of these notes has a completely different rhythm.

Penumbra Phantasm is NOT in THE HOLY.